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Last updated on 2026-08-19 23:51:37 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 3.57 | 226.51 | 230.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 2.28 | 224.50 | 226.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 180.02 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 180.83 | OK | |||
| r-devel-windows-x86_64 | 2.0.1 | 5.00 | 260.00 | 265.00 | OK | |
| r-patched-linux-x86_64 | 2.0.1 | 4.03 | 211.53 | 215.56 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 3.27 | 210.37 | 213.64 | OK | |
| r-release-macos-arm64 | 2.0.1 | 1.00 | 67.00 | 68.00 | OK | |
| r-release-macos-x86_64 | 2.0.1 | 3.00 | 195.00 | 198.00 | OK | |
| r-release-windows-x86_64 | 2.0.1 | 6.00 | 0.00 | 6.00 | OK | |
| r-oldrel-macos-arm64 | 2.0.1 | 1.00 | 37.00 | 38.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.0.1 | 3.00 | 199.00 | 202.00 | OK | |
| r-oldrel-windows-x86_64 | 2.0.1 | 7.00 | 160.00 | 167.00 | OK |
Version: 2.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘rEDM-tutorial.Rmd’ using rmarkdown
2026-08-20 05:34:02.117 R[42182:61630] XType: Using static font registry.
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...)
7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)
21: SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
24: eval(expr, envir)
25: eval(expr, envir)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd)
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
} if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) 4:
Traceback:
1: RowCumsum(valid)
2: FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, validLib = validLib, libOverlap = idx$libOverlap, backend = backend, verbose = verbose)
3: { watcher$capture_plot_and_output()SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)
4: ComputeError(predictions$Observations, predictions$Predictions)
5: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)ComputeError(predictions$Observations, predictions$Predictions)
6: cnd <- sanitize_call(cnd)FUN(X[[i]], ...) watcher$push(cnd) 5: switch(on_error, continue = invokeRestart("eval_continue"), SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp,
Traceback:
stop = invokeRestart("eval_stop"), error = NULL) 1: })
28: eval(call)
knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 29: embedded = embedded, validLib = validLib, noTime = noTime, eval(call)
ignoreNan = ignoreNan, backend = backend)$predictions)RowCumsum(valid) 7: lapply(X = S, FUN = FUN, ...)
2:
FindNeighbors(embedding, lib_i, pred_i, knn, exclusionRadius = exclusionRadius, 8: 30: doTryCatch(return(expr), name, parentenv, handler)with_handlers({ for (expr in tle$exprs) {
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
ev <- withVisible(eval(expr, envir))
6: FUN(X[[i]], ...)
watcher$capture_plot_and_output()11: validLib = validLib, libOverlap = idx$libOverlap, backend = backend, tryCatch(expr, error = function(e) { call <- conditionCall(e) verbose = verbose) 7:
watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
31: doWithOneRestart(return(expr), restart) 3:
SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, knn = knn, if (!is.null(call)) {lapply(X = S, FUN = FUN, ...)32: withOneRestart(expr, restarts[[1L]]) tau = tau, theta = th, exclusionRadius = exclusionRadius,
embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)33: 8:
4: withRestartList(expr, restarts[-nr]) if (identical(call[[1L]], quote(doTryCatch))) ComputeError(predictions$Observations, predictions$Predictions)
call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L)
prefix <- paste("Error in", dcall, ": ")doTryCatch(return(expr), name, parentenv, handler)
LONG <- 75L 5: sm <- strsplit(conditionMessage(e), "\n")[[1L]] 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: SweepRho(SMap(dataFrame, columns, target, lib, pred, E = E, Tp = Tp, 34: doWithOneRestart(return(expr), restart)
tryCatchList(expr, classes, parentenv, handlers) w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) knn = knn, tau = tau, theta = th, exclusionRadius = exclusionRadius, 35:
withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])11: tryCatch(expr, error = function(e) { w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b")
if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") embedded = embedded, validLib = validLib, noTime = noTime, ignoreNan = ignoreNan, backend = backend)$predictions)
6: FUN(X[[i]], ...) .Internal(seterrmessage(msg[1L])) call <- conditionCall(e) if (!silent && isTRUE(getOption("show.error.messages"))) { if (!is.null(call)) {
36: if (identical(call[[1L]], quote(doTryCatch))) withRestartList(expr, restarts) call <- sys.call(-4L) 7: dcall <- deparse(call, nlines = 1L)lapply(X = S, FUN = FUN, ...) cat(msg, file = outFile) .Internal(printDeferredWarnings()) prefix <- paste("Error in", dcall, ": ")
8: }doTryCatch(return(expr), name, parentenv, handler)
9:
LONG <- 75LtryCatchOne(expr, names, parentenv, handlers[[1L]])
10: sm <- strsplit(conditionMessage(e), "\n")[[1L]]tryCatchList(expr, classes, parentenv, handlers)37: w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) if (is.na(w)) watcher$capture_plot_and_output() w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], invisible(structure(msg, class = "try-error", condition = e))})
watcher$print_value(ev$value, ev$visible, envir)12:
try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
13: }sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) type = "b") TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
14: FUN(X[[i]], ...)
15: lapply(seq_len(cores), inner.do)
if (w > LONG) 11: prefix <- paste0(prefix, "\n ")16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
} else prefix <- "Error : "
17: tryCatch(expr, error = function(e) {doTryCatch(return(expr), name, parentenv, handler)
38: evaluate::evaluate(...) call <- conditionCall(e) msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e)) if (!is.null(call)) {18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20:
})39:
tryCatch(parallel::mclapply(values, worker, mc.cores = cores, 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) try(lapply(X = S, FUN = FUN, ...), silent = TRUE) keep_message = if (is.numeric(options$message)) TRUE else options$message, w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], stop_on_error = if (is.numeric(options$error)) options$error else { type = "b")
13: mc.preschedule = TRUE), error = function(e) NULL)sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
if (w > LONG) prefix <- paste0(prefix, "\n ")21:
}SweepApply(theta, worker, numProcess) else prefix <- "Error : " if (options$error && options$include) 0L
msg <- paste0(prefix, conditionMessage(e), "\n")14: FUN(X[[i]], ...)
else 2L }, output_handler = knit_handlers(options$render, options))
40: 15: .Internal(seterrmessage(msg[1L]))lapply(seq_len(cores), inner.do)22: in_dir(input_dir(), expr) if (!silent && isTRUE(getOption("show.error.messages"))) {unlist(SweepApply(theta, worker, numProcess))
cat(msg, file = outFile) .Internal(printDeferredWarnings())
}41: in_input_dir(evaluate(code, envir = env, new_device = FALSE,
16: parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE)
17: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)doTryCatch(return(expr), name, parentenv, handler)
if (options$error && options$include) invisible(structure(msg, class = "try-error", condition = e))24: })
18: eval(expr, envir)
tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: 0L else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)12: 25:
43: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)tryCatchList(expr, classes, parentenv, handlers)eval(expr, envir)
20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE), error = function(e) NULL)block_exec(params)
21:
SweepApply(theta, worker, numProcess)
22: 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
14: FUN(X[[i]], ...)
26: unlist(SweepApply(theta, worker, numProcess))15: withVisible(eval(expr, envir))44:
27: call_block(x)withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output()
23: lapply(seq_len(cores), inner.do)PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis",
target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE)
if (on_message$capture) {45: 16: 24: watcher$push(cnd)process_group(group)eval(expr, envir)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), parallel::mclapply(values, worker, mc.cores = cores, mc.preschedule = TRUE) error = function(e) { if (progress && is.function(pb$interrupt))
}17: if (on_message$silence) {
invokeRestart("muffleMessage")doTryCatch(return(expr), name, parentenv, handler) pb$interrupt()
18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) } if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
25: 19: tryCatchList(expr, classes, parentenv, handlers)47:
}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return()with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), } watcher$capture_plot_and_output()eval(expr, envir) if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)
26: withVisible(eval(expr, envir))
27: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { error = function(e) { } watcher$capture_plot_and_output() if (on_warning$silence) { invokeRestart("muffleWarning") } if (progress && is.function(pb$interrupt)) if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() pb$interrupt()}, error = function (cnd) if (is_R_CMD_build() || is_R_CMD_check()) } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))20: tryCatch(parallel::mclapply(values, worker, mc.cores = cores, switch(on_error, continue = invokeRestart("eval_continue"),
stop = invokeRestart("eval_stop"), error = NULL) mc.preschedule = TRUE), error = function(e) NULL){})48:
xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 21: watcher$capture_plot_and_output() error = function(e) { cnd <- sanitize_call(cnd)
if (progress && is.function(pb$interrupt)) SweepApply(theta, worker, numProcess)
22: unlist(SweepApply(theta, worker, numProcess))
23: PredictNonlinear(dataFrame = Thrips, columns = "Thrips_imaginis", pb$interrupt() watcher$push(cnd) if (is_R_CMD_build() || is_R_CMD_check()) switch(on_error, continue = invokeRestart("eval_continue"), target = "Thrips_imaginis", lib = "1 73", pred = "1 73", E = E, showPlot = TRUE) error <<- format(e) stop = invokeRestart("eval_stop"), error = NULL) }), list(rlang_trace_top_env = knit_global())), function(loc) {
})
24: 28: setwd(wd)eval(expr, envir)
25: eval(call)eval(expr, envir)28: eval(call)
write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) 26: 29:
withVisible(eval(expr, envir))29:
27: eval(call)withCallingHandlers(code, error = function (e) eval(call)
paste0("\n", rule(), error, "\n", rule()))
}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
30: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir))49: process_file(text, output)
rlang::entrace(e), message = function (cnd) {50: watcher$capture_plot_and_output()knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE if (on_message$capture) {}, handlers)
31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]]) watcher$push(cnd)30: with_handlers({
for (expr in tle$exprs) { } ev <- withVisible(eval(expr, envir)) if (on_message$silence) { invokeRestart("muffleMessage")
watcher$capture_plot_and_output() }51: watcher$print_value(ev$value, ev$visible, envir) }rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), TRUE33: }, warning = function (cnd) output_dir = getwd(), ...)}, handlers){withRestartList(expr, restarts[-nr]) if (getOption("warn") >= 2 || getOption("warn") < 0) {
return()34: 52: vweave_rmarkdown(...)
53: }engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
36: withRestartList(expr, restarts)
37: withRestarts(with_handlers({55: watcher$capture_plot_and_output()
if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd)tryCatchOne(expr, names, parentenv, handlers[[1L]]) for (expr in tle$exprs) {31: doWithOneRestart(return(expr), restart)
32: withOneRestart(expr, restarts[[1L]])
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)
}56: tryCatchList(expr, classes, parentenv, handlers) TRUE33: }, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE) } if (on_warning$silence) {
withRestartList(expr, restarts[-nr]) invokeRestart("muffleWarning")
38:
57: tryCatch({34: engine$weave(file, quiet = quiet, encoding = enc)doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
}evaluate::evaluate(...) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {36: 39: texi2pdf(file = output, clean = FALSE, quiet = quiet)}, error = function (cnd) withRestartList(expr, restarts){ output <- find_vignette_product(name, by = "texi2pdf", engine = engine)evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, } outputs <- c(outputs, output)}, error = function(e) { keep_message = if (is.numeric(options$message)) TRUE else options$message, thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", stop_on_error = if (is.numeric(options$error)) options$error else { watcher$capture_plot_and_output() file, conditionMessage(e))) if (options$error && options$include) 0L})
37: withRestarts(with_handlers({ cnd <- sanitize_call(cnd) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir))58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", watcher$capture_plot_and_output() else 2L watcher$print_value(ev$value, ev$visible, envir) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), } stop = invokeRestart("eval_stop"), error = NULL) }, output_handler = knit_handlers(options$render, options)) TRUE skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpgiNPhR/file6ab727fafcda.rds")
})}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
38:
28: eval(call)
40: 29: evaluate::evaluate(...)
39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, An irrecoverable exception occurred. R is aborting now ...
in_dir(input_dir(), expr) keep_message = if (is.numeric(options$message)) TRUE else options$message, eval(call) stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 0L41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) else 2L
}, output_handler = knit_handlers(options$render, options)))30: with_handlers({ for (expr in tle$exprs) {40: in_dir(input_dir(), expr)
42:
41: eng_r(options)
43: ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir)block_exec(params) }
44: TRUEcall_block(x)}, handlers)in_input_dir(evaluate(code, envir = env, new_device = FALSE,
31: doWithOneRestart(return(expr), restart)
32: keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include)
45: process_group(group)
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) withOneRestart(expr, restarts[[1L]]) error <<- format(e)
33: withRestartList(expr, restarts[-nr])
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
0L36: })
withRestartList(expr, restarts)47: else 2L }, output_handler = knit_handlers(options$render, options)))
42: eng_r(options)
43: block_exec(params)
44: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) 37: pb$interrupt()call_block(x) if (is_R_CMD_build() || is_R_CMD_check()) withRestarts(with_handlers({ error <<- format(e) for (expr in tle$exprs) {
ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
}), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 45: error = function(e) {38: evaluate::evaluate(...)
if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd)39: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, process_group(group) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule())) keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else {}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
40: in_dir(input_dir(), expr)49: 46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) {process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51:
41: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, if (progress && is.function(pb$interrupt)) pb$interrupt()rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
if (is_R_CMD_build() || is_R_CMD_check()) 42: error <<- format(e)eng_r(options)
52: vweave_rmarkdown(...)
53: })43: block_exec(params)
engine$weave(file, quiet = quiet, encoding = enc)47:
54:
doTryCatch(return(expr), name, parentenv, handler)44:
with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), call_block(x)55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc) error = function(e) {45: setwd(startdir)process_group(group) if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check())
46: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) error <<- format(e) }) output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", 47: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) engine = engine) }), list(rlang_trace_top_env = knit_global()))
48: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { error <<- format(e) if (progress && is.function(pb$interrupt)) } }), list(rlang_trace_top_env = knit_global()))
48: outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSExfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), pb$interrupt() error = function(e) { fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e))) if (is_R_CMD_build() || is_R_CMD_check()) if (progress && is.function(pb$interrupt)) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) })
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpgiNPhR/file6ab727fafcda.rds") error <<- format(e)
An irrecoverable exception occurred. R is aborting now ...
}), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: vweave_rmarkdown(...) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
49: process_file(text, output)
50: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
51: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
52: 53: engine$weave(file, quiet = quiet, encoding = enc)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]])
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc)vweave_rmarkdown(...)
53: engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet)
54: doTryCatch(return(expr), name, parentenv, handler)
55: tryCatchOne(expr, names, parentenv, handlers[[1L]]) output <- find_vignette_product(name, by = "texi2pdf",
56: tryCatchList(expr, classes, parentenv, handlers)
57: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpgiNPhR/file6ab727fafcda.rds")
An irrecoverable exception occurred. R is aborting now ...
outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
58: tools::buildVignettes(dir = "/Volumes/Builds/packages/big-sur-arm64/results/4.5/rEDM.Rcheck/vign_test/rEDM", skip = TRUE, ser_elibs = "/Volumes/Temp/tmp/RtmpgiNPhR/file6ab727fafcda.rds")
An irrecoverable exception occurred. R is aborting now ...
Quitting from rEDM-tutorial.Rmd:466-469 [smap_thrips]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `data.frame()`:
! arguments imply differing number of rows: 15, 0
---
Backtrace:
▆
1. └─rEDM::PredictNonlinear(...)
2. └─base::data.frame(Theta = theta, rho = rho)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'rEDM-tutorial.Rmd' failed with diagnostics:
arguments imply differing number of rows: 15, 0
--- failed re-building ‘rEDM-tutorial.Rmd’
SUMMARY: processing the following file failed:
‘rEDM-tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
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